Thanks to visit codestin.com
Credit goes to github.com

Skip to content

Adding upd #364

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Merged
merged 13 commits into from
Jun 26, 2023
Merged

Adding upd #364

merged 13 commits into from
Jun 26, 2023

Conversation

@hrydbeck
Copy link
Contributor

@hrydbeck hrydbeck commented Jun 21, 2023 •
edited
Loading

This PR adds a UPD caller to nf-core raredisease

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/raredisease branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

hrydbeck added 7 commits June 15, 2023 09:49
@hrydbeck
Added module upd
1acc542 
Copied upd folder from nf-core/modules/modules
@hrydbeck
Added upd.config
30bff03
@hrydbeck
included upd.config
f9a3994 
Added line to include upd.config
@hrydbeck
Added description of output
613d7e0 
Added description to output.md
@hrydbeck
nf-core modules install --force upd
2f80fcd 
Added upd to:
modules.json and annotate_snvs.config
and included in annotate_snvs.nf
@hrydbeck
Merge branch 'dev' of https://github.com/nf-core/raredisease into add…
39c84da 
…ing_upd
@hrydbeck
add upd to subworkflow
a1ab7ed
@github-actions
Copy link

github-actions bot commented Jun 21, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 13eec8f

+| ✅ 156 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-06-26 07:20:44

@ramprasadn ramprasadn requested a review from jemten June 22, 2023 11:59
jemten
jemten reviewed Jun 22, 2023
View reviewed changes
Copy link
Collaborator

@jemten jemten left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Nice work both! I believe that the output from upd isn't necessary sorted so it could be good to stream the output of upd into sort. Needed, if we want to convert the bed file to big bed downstream.

@ramprasadn
Copy link
Collaborator

ramprasadn commented Jun 26, 2023

Good point @jemten.. I have updated the script in the upd module, and the default output will be a sorted bed file now.

@ramprasadn ramprasadn requested a review from jemten June 26, 2023 07:38
jemten
jemten approved these changes Jun 26, 2023
View reviewed changes
Copy link
Collaborator

@jemten jemten left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

🌟

@hrydbeck hrydbeck merged commit f5ccf9c into nf-core:dev Jun 26, 2023
@hrydbeck hrydbeck deleted the adding_upd branch September 6, 2023 14:04
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@jemten jemten jemten approved these changes

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

3 participants

@hrydbeck @ramprasadn @jemten